verbose = False
dry_run = False
show_script = False
show_defaults = False
test_mode = False
phaser {
mode = ANO EP_AUTO EP_SAD *MR_AUTO MR_BRF MR_BTF MR_FRF MR_FTF MR_LLG \
MR_PAK MR_RNP NMA
sad_mode = *SAD MR_SAD
hklin = None
labin = None
crystal {
xtal_id = None
pdb_file = None
ha_file = None
dataset {
wave_id = None
hklin = None
labin = None
wavelength = None
energy = None
}
}
crystal_symmetry {
unit_cell = None
space_group = None
}
composition {
solvent = None
chain {
chain_type = *protein na
sequence_file = None
sequence = None
nres = None
mw = None
num = 1
}
atom {
element = None
num = None
}
}
ensemble {
model_id = None
coordinates {
pdb = None
rmsd = None
identity = None
}
map_hklin = None
map_labels = None
map_extent = None
map_rms = 1.0
map_centre = None
map_protein_mw = 0
map_nucleic_mw = 0
fractional_comp = none
}
search {
ensembles = None
copies = 1
}
solution = None
output_dir = None
keywords {
general {
root = "PHASER"
title = "[no title set]"
verbose = None
debug = None
mute = None
xyzout = None
hklout = None
jobs = 2
}
atoms {
change_scatterer = False
change_scatterer_type = "Se"
change_bfac_wilson = False
}
bfactor {
wilson_restraint = True
wilson_sigma = 5
sphericity_restraint = True
sphericity_sigma = 5
refine_restraint = True
refine_sigma = 10
}
bins {
minimum = 6
maximum = 50
width = 500
cubic = 0,1,0
}
boxscale = 4.0
clmn {
sphere = 0
lmin = 4
lmax = 100
}
cluster_pdb {
id = None
file_name = None
}
eigen {
read = None
write = True
}
ffts {
minimum = 20
maximum = 80
}
hand = off on *both
integration {
fixed = False
step = None
}
llgcompletion {
complete = True
scatterer = None
clash = 0
sigma = 6
ncycle = 50
maps = False
}
macano {
protocol = *default off custom
macrocycle {
ref_anis = None
ref_bins = None
ref_solk = None
ref_solb = None
ncycle = None
minimiser = *BFGS NEWTON DESCENT
}
}
macmr {
protocol = *default off custom
macrocycle {
ref_rota = None
ref_tran = None
ref_bfac = None
ref_vrms = None
ncycle = None
minimizer = *BFGS NEWTON DESCENT
}
}
macsad {
protocol = *default off custom
macrocycle {
ref_k = None
ref_b = None
ref_sigma = None
ref_xyz = None
ref_occ = None
ref_bfac = None
ref_fdp = None
ref_sa = None
ref_sb = None
ref_sp = None
ref_sd = None
ncycle = None
minimizer = *bfgs newton descent
}
}
nmamethod {
oscillators = *rtb ca all
rtb_maxblocks = 125
rtb_nresidues = 0
radius = 5
force = 1
}
nmapdb {
mode = None
combination = None
perturb = *rms dq
rms {
step = None
stretch = None
clash = None
maxrms = None
direction = *forward backward tofro
}
dq = None
}
normalization {
bins = None
aniso = None
solk = None
solb = None
}
outlier {
reject = True
probability = 1e-06
}
pack {
select = *percent best allow all
cutoff = 5
quick = True
distance = 3.0
}
partial {
pdb = None
hklin = None
variance = rms *id
deviation = None
}
peaks_rotation {
select = *percent sigma number all
cutoff = 75
cluster = True
}
peaks_translation {
select = *percent sigma number all
cutoff = 75
cluster = True
}
permutations = False
ptgroup {
coverage = 0.90
identity = 0.95
rmsd = 1.00
tolerance_angular = 0.035
tolerance_spatial = 0.5
}
purge {
enable = True
percent = 0.75
}
rescore_rotation = True
rescore_translation = True
resharpen_percent = 100
resolution {
high = None
low = None
auto {
high = None
low = None
}
}
rotate {
volume = *full around
euler = None
range = None
}
sampling_rotation = None
sampling_translation = None
scattering {
scatterer {
type = None
fp = None
fdp = None
fixfdp = *EDGE ON OFF
}
restraint = True
sigma = 0.2
}
search_order_auto = True
search_method = *full fast
sgalternative {
select = all *hand list none
test = None
sort = True
}
solparameters {
fsol = 0.95
bsol = 300
}
solution_origin_ensemble = None
sort = None
target_frf = *lerf1 lerf2 crowther
target_ftf = *letf1 letf2 correlation
topfiles = 1
translate {
volume = *full line region around
fractional = None
start = None
end = None
range = None
}
zscore_solved = 8
}
}